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Yorodumi- PDB-8p84: X-ray structure of Thermoanaerobacterales bacterium monoamine oxidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p84 | ||||||
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Title | X-ray structure of Thermoanaerobacterales bacterium monoamine oxidase | ||||||
Components | Monoamine oxidase | ||||||
Keywords | FLAVOPROTEIN / monoamine oxidase / Thermoanaerobacterales bacterium / enzyme / n-hexylamine | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||
Biological species | Thermoanaerobacterales bacterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Basile, L. / Santema, L.L. / Fraaije, M.W. / Binda, C. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Febs J. / Year: 2024 Title: Discovery and structural characterization of a thermostable bacterial monoamine oxidase. Authors: Santema, L.L. / Basile, L. / Binda, C. / Fraaije, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8p84.cif.gz | 199.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p84.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 8p84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/8p84 ftp://data.pdbj.org/pub/pdb/validation_reports/p8/8p84 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 50089.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterales bacterium (bacteria) Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG4000, 100 mM tris buffer pH 8.5, 200 mM magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.13 Å / Num. obs: 131032 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.033 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.158 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6419 / CC1/2: 0.689 / Rpim(I) all: 0.709 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→47.13 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.297 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.618 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→47.13 Å
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Refine LS restraints |
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